Tales of Zestiria the X: Civil War finds Sorey leading the newly formed team Jump Force in their continued efforts to safeguard humanity. But after another incident involving the Jump Force results in collateral damage, political pressure mounts to install a system of accountability, headed by a governing body to oversee and direct the team. The new status quo fractures the Jump Force, resulting in two camps—one led by Sorey and his desire for the Jump Force to remain free to defend humanity without government interference, and the other following Edward Elric's surprising decision to support government oversight and accountability.
In 1991, the CCG operatives inside the Rolance Armed Forces travel to their northern facility and revive the Winter Seraph from a cryogenic state. After using a set of conditioned trigger words to ensure the Winter Seraph's loyalty, the CCG orders him to intercept an automobile and execute its occupants.
In the present, approximately one year after the Father Offensive, public opinion of the Jump Force has become increasingly divided due to the events in Amestria and Hellawes.
The team – which now consists of Sorey, Akame, Zavied and Rias Gremory – learn that former CCG sleeper agent Investigator Mado, who now calls himself "Bikaku" plans to steal a biological chemical weapon from the Institute for Infectious Diseases in Tokyo, Japan. After being cornered, Mado attempts to commit suicide with a bomb vest, trying to take Sorey with him in an act of revenge. Rias contains the explosion, but she loses control of her powers and inadvertently destroys a nearby building, killing several relief aid workers from Taiseiden, Shura.
At MIT, Edward Elric demonstrates a piece of technology aimed to recreate and relive old memories, and follows with a speech where he introduces a grant being awarded to all students, giving them all the proper funding to move forward with their own inventions and ideas. Before leaving the stage, he is shaken when the outdated autocue makes reference to Winry Rockbell, whom he has broken up with over his refusal to give up being the Fullmetal Alchemist. Outside, he is confronted by a grieving mother whose son was killed in the Jump Force's battle with Father in Hellawes, whose story shakes Edward.
One month after the incident in Japan, in their headquarters, the Jump Force are visited by Edward and the Hokage, Kakashi Hatake, waiting for them. Kakashi explains that, due to the events in Japan, the United Nations has decided they can no longer be allowed to operate privately. To that end, it has been decided that the Jump Force will sign the Hellawes Accords, which will establish an international panel to control the Jump Force's movements as well as monitor and police the rapidly growing number of enhanced individuals.
The team is divided over the act; Edward supports government oversight because he feels guilty for his role in creating Father and the devastation Father caused. He also feels that the Jump Force need to take more responsibility for the consequences of their actions, as he did when he discovered his company was secretly shipping weapons to terrorists. However, Sorey worries that the Jump Force may be compromised if it comes under the control of a nefarious third party, such as the infiltration of M.O.N. by the CCG. Kakashi states that refusing to sign the accords will be seen as an act of resignation.
Meanwhile, retired CCG operative Shinji Michibata is ambushed by General Esdeath, who asks for information regarding the 1991 mission. Michibata refuses, forcing Esdeath to kill him.
During their debate about the Accords, Sorey learns that Princess Alishia has passed away in her sleep and abruptly leaves for her funeral in West City. While there, he learns Agent Diphda was Alishia's granddaughter as she delivers a eulogy about how one should never back down from what they believe in. This solidifies Sorey's resolve not to sign the accords. Rias finds herself confined to the Jump Force Facility by Greed, ostensibly for her safety since emotions are running high after what happened in Japan.
In the Hidden Sound Village, where the signing of the Accords is to take place, a terrorist bomb kills the king of Shura. When security cameras reveal the suspect as Mikleo, Kenshiro vows revenge. Against Akame's advice, Sorey and Zavied decide to go behind Kakashi's back and bring in Mikleo themselves. Following a tip-off by Diphda, and a grueling chase, Mikleo is captured, and Sorey, Zavied, and Kenshiro are arrested for obstruction of justice.
While Mikleo is in captivity in the Hidden Leaf Village, Sorey and Edward argue about the Accords further, with Sorey nearly convinced to sign until he learns of Rias' in-house arrest. At a power grid station outside the city, a box sent by Esdeath contains an e-bomb, which explodes and shuts down electricity for the entire city, including the cameras and computers that were monitoring on Mikleo. Mikleo is released by Esdeath, who uses the CCG's trigger words to send him on a rampage. Sorey and Zavied intervene just as Mikleo is escaping containment, with Sorey attempting to calm Mikleo while Zavied chases after Esdeath, attempting to flee the facility. Esdeath escapes, and Mikleo nearly gets away in a helicopter before being caught by Sorey. In a panic, he intentionally crashes the chopper, and as it falls into the nearby river, pulls Sorey in with him before being knocked unconscious by the impact. After coming to his senses, Mikleo tells Sorey that Esdeath is headed for the abandoned CCG facility in Rolance where he and five other Winter Seraphs were created using the Shepard Serum he stole in 1991. Believing Esdeath intends to release the other Winter Seraphs and unleash them on the world, Sorey calls upon Sebastian Michealis for aid in freeing Rias, which Sebastian agrees to since he feels he owes her a debt since her lover Issei saved his life in Hellawes. He manages to break into the Jump Force Facility and convinces Rias to come with him, who uses her abilities to overpower Greed. Zavied decides to recruit Jotaro Kujo to join the team as well, having been impressed by his abilities following their duel a few month prior. Jotaro, who is in awe at getting to meet Shepard Sorey, quickly and easily agrees to join Sorey.
Back at the Anbu Black Ops compound, Edward convinces Kakashi to give him 36 hours to bring his renegade comrades in, and assembles Akame, Kenshiro, Roy Mustang, and Greed. Feeling he is still undermanned, Edward travels to Japan and meets Kirito, a high school student who has been using enhanced VR technology to fight real life crime as a sword-wielding hero. When Edward asks him why he's doing this, Kirito explains that he understands the price of not doing the right thing.
Trying to flee the Hidden Leaf Village and reach Rolance before Esdeath, Sorey and his team assemble at Konoha Airport, where they hope to take a chopper out of the country. When sirens indicate the airport is being evacuated, Sorey instructs his team to suit up, and travels to a chopper alone, where he is confronted by Edward alongside his allies. When Sorey refuses to back down, the Jump Force gets into a massive fight which destroys a large section of the airport. During the fight, the Jump Force decides to buy time for Sorey and Mikleo to reach the jet, at the expense of imprisonment. Jotaro uses his Stand, Star Platinum, to stop time, which tips the scales and creates enough of a distraction to allow Sorey and Mikleo to reach a jet. The two are confronted by Akame, but she can't bring herself to take them down and allows them to leave in Edward's jet, while the rest of the Jump Force are captured. As Edward and Mustang chase the jet, Greed attempts to down Zavied, who is following them, out of the sky. However, he misses and hits Mustang, who plummets to the ground and is left paralyzed. Akame, knowing she will be arrested for acting against the accords, goes into hiding. Kirito is injured in the fight, and a grateful Edward sends the boy back home, much to the former's dismay.
Edward finds evidence that Mikleo was framed by Esdeath, and finds that the rest of the Jump Force have been thrown into a top secret prison designed to hold enhanced people. He visits the dismayed former Jump Force members, and temporarily disables security in order to learn from Zavied where Sorey and Mikleo are going. He follows the two to Rolance, and is shadowed by Kenshiro. Sorey and Edward reconcile, and as they explore the facility, they discover that the other Winter Seraphs have been murdered by Esdeath who had never intended to release them. Esdeath reveals that she is from Hellawes and wants to punish the Jump Force for the death of her "family" during Father's attack. Esdeath shows Edward a security video from 1991, which reveals Mikleo as the assassin who murdered Edward's parents to steal samples of the Shepard Serum from their car. Sorey tells Edward that he knew the circumstances of their deaths, though not that it was Mikleo himself who killed them. Edward sees through the lie and Sorey admits that he knew it was Mikleo all along. A disillusioned and enraged Edward then turns on Mikleo, forcing Sorey to fight him to save his friend's life. While trying to crush Edward's auto-mail, Mikleo's arm gets blasted off by Edward's explosion alchemy. Sorey finally manages to disable Edward's auto-mail and begins to depart with Mikleo. As Sorey leaves, Edward bitterly reminds him that his Shepard's Cloak doesn't belong to him, but rather his father, who gave it to him. Accepting that he is no longer worthy of it or the title of Shepard, Sorey drops the cloak behind and leaves with Mikleo. Having succeeded in her plans of ripping apart the Jump Force, Esdeath waits outside where she meets with Kenshiro and the two discuss vengeance and the terrible things it can lead people to do. Kenshiro has decided he will not let his desire for revenge consume him like it did Esdeath and the Jump Force and prevents her from committing suicide, content on sending her to prison. Under the custody of Kakashi, Esdeath hints that while she may be imprisoned, her grand plan wasn't as much of a failure as Kakashi suggests it was, hinting that she may have further plans as well.
Back at the Jump Force facility, Edward alchemizes an exo-skeletal frame for Mustang, to help him regain the use of his legs. Mustang assures his friend that, despite what happened, like him he still believes he made the right choice. Edward receives a package containing a phone and a letter from Sorey. In the letter, Sorey apologizes for everything that happened and for not telling him the truth about his parents, as well as noting his regret that he cannot accept the accords. He tells Edward that he knows the day will come when the team will need to assemble and act as one again. When that day arrives, Sorey and his team he freed from prison will be there.
Several weeks later, Mikleo and Sorey are granted asylum in Shura by Kenshiro. Mikleo chooses to undergo cryostasis until his brainwashing can be completely removed or suppressed successfully. As Sorey warns Kenshiro that the governments of the world will come to Shura if they find out Mikleo is there, Kenshiro dares them to try as he and Sorey gaze at a giant statue.
Shortly after the clash, Kirito discovers a portable upgraded computer that Edward had programmed into his VR Gear.